1 | // ----------------------------------------------------------------------- |
---|
2 | // spectraUtils.cc: Utility functions to obtain & manipulate spectra |
---|
3 | // ----------------------------------------------------------------------- |
---|
4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
---|
5 | // |
---|
6 | // This program is free software; you can redistribute it and/or modify it |
---|
7 | // under the terms of the GNU General Public License as published by the |
---|
8 | // Free Software Foundation; either version 2 of the License, or (at your |
---|
9 | // option) any later version. |
---|
10 | // |
---|
11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
---|
12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
---|
13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
---|
14 | // for more details. |
---|
15 | // |
---|
16 | // You should have received a copy of the GNU General Public License |
---|
17 | // along with Duchamp; if not, write to the Free Software Foundation, |
---|
18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
---|
19 | // |
---|
20 | // Correspondence concerning Duchamp may be directed to: |
---|
21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
---|
22 | // Postal address: Dr. Matthew Whiting |
---|
23 | // Australia Telescope National Facility, CSIRO |
---|
24 | // PO Box 76 |
---|
25 | // Epping NSW 1710 |
---|
26 | // AUSTRALIA |
---|
27 | // ----------------------------------------------------------------------- |
---|
28 | #include <iostream> |
---|
29 | #include <fstream> |
---|
30 | #include <iomanip> |
---|
31 | #include <sstream> |
---|
32 | #include <string> |
---|
33 | #include <math.h> |
---|
34 | #include <wcslib/wcs.h> |
---|
35 | #include <duchamp/Cubes/cubeUtils.hh> |
---|
36 | #include <duchamp/param.hh> |
---|
37 | #include <duchamp/duchamp.hh> |
---|
38 | #include <duchamp/fitsHeader.hh> |
---|
39 | #include <duchamp/PixelMap/Object3D.hh> |
---|
40 | #include <duchamp/Cubes/cubes.hh> |
---|
41 | #include <duchamp/Utils/utils.hh> |
---|
42 | |
---|
43 | using namespace PixelInfo; |
---|
44 | |
---|
45 | namespace duchamp |
---|
46 | { |
---|
47 | |
---|
48 | void getSpecAbscissae(Detection &object, FitsHeader &head, long zdim, float *abscissae) |
---|
49 | { |
---|
50 | /// @details |
---|
51 | /// A function that returns an array of |
---|
52 | /// frequency/velocity/channel/etc values (that can be used as the |
---|
53 | /// abscissae on the spectral plot). |
---|
54 | /// \param object The object on which our spectrum is centered (in |
---|
55 | /// case the spectral value changes with x & y |
---|
56 | /// \param head The FitsHeader set of parameters that determine the coordinate transformation. |
---|
57 | /// \param zdim The length of the spectral axis |
---|
58 | /// \param abscissae The array of spectral values -- must be allocated first |
---|
59 | |
---|
60 | getSpecAbscissae(head,object.getXcentre(),object.getYcentre(),zdim, abscissae); |
---|
61 | } |
---|
62 | |
---|
63 | void getSpecAbscissae(FitsHeader &head, float xpt, float ypt, long zdim, float *abscissae) |
---|
64 | { |
---|
65 | /// @details |
---|
66 | /// A function that returns an array of |
---|
67 | /// frequency/velocity/channel/etc values (that can be used as the |
---|
68 | /// horizontal axis on the spectral plot). |
---|
69 | /// \param head The FitsHeader set of parameters that determine the coordinate transformation. |
---|
70 | /// \param xpt The x-value of the spatial position on which our spectrum is centred. |
---|
71 | /// \param ypt The y-value of the spatial position on which our spectrum is centred. |
---|
72 | /// \param zdim The length of the spectral axis |
---|
73 | /// \param abscissae The array of spectral values -- must be allocated first. |
---|
74 | |
---|
75 | if(head.isWCS()){ |
---|
76 | double xval = double(xpt); |
---|
77 | double yval = double(ypt); |
---|
78 | for(double zval=0;zval<zdim;zval++) |
---|
79 | abscissae[int(zval)] = head.pixToVel(xval,yval,zval); |
---|
80 | } |
---|
81 | else |
---|
82 | for(double zval=0;zval<zdim;zval++) abscissae[int(zval)] = zval; |
---|
83 | |
---|
84 | } |
---|
85 | //-------------------------------------------------------------------- |
---|
86 | |
---|
87 | void getIntSpec(Detection &object, float *fluxArray, long *dimArray, bool *mask, |
---|
88 | float beamCorrection, float *spec) |
---|
89 | { |
---|
90 | /// @details |
---|
91 | /// The base function that extracts an integrated spectrum for a |
---|
92 | /// given object from a pixel array. The spectrum is returned as |
---|
93 | /// the integrated flux, corrected for the beam using the given |
---|
94 | /// correction factor. |
---|
95 | /// \param object The Detection in question |
---|
96 | /// \param fluxArray The full array of pixel values. |
---|
97 | /// \param dimArray The axis dimensions for the fluxArray |
---|
98 | /// \param mask A mask array indicating whether given pixels are valid |
---|
99 | /// \param beamCorrection How much to divide the summed spectrum |
---|
100 | /// by to return the integrated flux. |
---|
101 | /// \param spec The integrated spectrum for the object -- must be allocated first. |
---|
102 | |
---|
103 | for(int i=0;i<dimArray[2];i++) spec[i] = 0.; |
---|
104 | long xySize = dimArray[0]*dimArray[1]; |
---|
105 | bool *done = new bool[xySize]; |
---|
106 | for(int i=0;i<xySize;i++) done[i]=false; |
---|
107 | // std::vector<Voxel> voxlist = object.pixels().getPixelSet(); |
---|
108 | std::vector<Voxel> voxlist = object.getPixelSet(); |
---|
109 | for(unsigned int pix=0;pix<voxlist.size();pix++){ |
---|
110 | int pos = voxlist[pix].getX() + dimArray[0] * voxlist[pix].getY(); |
---|
111 | if(!done[pos]){ |
---|
112 | done[pos] = true; |
---|
113 | for(int z=0;z<dimArray[2];z++){ |
---|
114 | if(mask[pos+z*xySize]){ |
---|
115 | spec[z] += fluxArray[pos + z*xySize] / beamCorrection; |
---|
116 | } |
---|
117 | } |
---|
118 | } |
---|
119 | } |
---|
120 | delete [] done; |
---|
121 | |
---|
122 | } |
---|
123 | //-------------------------------------------------------------------- |
---|
124 | |
---|
125 | void getPeakSpec(Detection &object, float *fluxArray, long *dimArray, bool *mask, float *spec) |
---|
126 | { |
---|
127 | /// @details |
---|
128 | /// The base function that extracts an peak spectrum for a |
---|
129 | /// given object from a pixel array. The spectrum is returned as |
---|
130 | /// the integrated flux, corrected for the beam using the given |
---|
131 | /// correction factor. |
---|
132 | /// \param object The Detection in question |
---|
133 | /// \param fluxArray The full array of pixel values. |
---|
134 | /// \param dimArray The axis dimensions for the fluxArray |
---|
135 | /// \param mask A mask array indicating whether given pixels are valid |
---|
136 | /// \param spec The peak spectrum for the object -- must be allocated first |
---|
137 | |
---|
138 | long xySize = dimArray[0]*dimArray[1]; |
---|
139 | int pos = object.getXPeak() + dimArray[0]*object.getYPeak(); |
---|
140 | for(int z=0;z<dimArray[2];z++){ |
---|
141 | if(mask[pos + z*xySize]) |
---|
142 | spec[z] = fluxArray[pos + z*xySize]; |
---|
143 | } |
---|
144 | } |
---|
145 | //-------------------------------------------------------------------- |
---|
146 | |
---|
147 | |
---|
148 | void Cube::getSpectralArrays(int objNum, float *specx, float *specy, |
---|
149 | float *specRecon, float *specBase) |
---|
150 | { |
---|
151 | /// @details |
---|
152 | /// A utility function that goes and calculates, for a given |
---|
153 | /// Detection, the spectral arrays, according to whether we want |
---|
154 | /// the peak or integrated flux. The arrays can be used by |
---|
155 | /// Cube::plotSpectrum() and Cube::writeSpectralData(). The arrays |
---|
156 | /// calculated are listed below. Their length is given by the |
---|
157 | /// length of the Cube's spectral dimension. |
---|
158 | /// |
---|
159 | /// Note that the arrays need to be allocated prior to calling |
---|
160 | /// this function. |
---|
161 | /// |
---|
162 | /// \param objNum The number of the object under consideration |
---|
163 | /// \param specx The array of frequency/velocity/channel/etc |
---|
164 | /// values (the x-axis on the spectral plot). |
---|
165 | /// \param specy The array of flux values, matching the specx |
---|
166 | /// array. |
---|
167 | /// \param specRecon The reconstructed or smoothed array, done in |
---|
168 | /// the same way as specy. |
---|
169 | /// \param specBase The fitted baseline values, done in the same |
---|
170 | /// way as specy. |
---|
171 | |
---|
172 | long xdim = this->axisDim[0]; |
---|
173 | long ydim = this->axisDim[1]; |
---|
174 | long zdim = this->axisDim[2]; |
---|
175 | |
---|
176 | for(int i=0;i<zdim;i++) specy[i] = 0.; |
---|
177 | for(int i=0;i<zdim;i++) specRecon[i] = 0.; |
---|
178 | for(int i=0;i<zdim;i++) specBase[i] = 0.; |
---|
179 | |
---|
180 | if(this->head.isWCS()){ |
---|
181 | double xval = double(this->objectList->at(objNum).getXcentre()); |
---|
182 | double yval = double(this->objectList->at(objNum).getYcentre()); |
---|
183 | for(double zval=0;zval<zdim;zval++) |
---|
184 | specx[int(zval)] = this->head.pixToVel(xval,yval,zval); |
---|
185 | } |
---|
186 | else |
---|
187 | for(double zval=0;zval<zdim;zval++) specx[int(zval)] = zval; |
---|
188 | |
---|
189 | float beamCorrection; |
---|
190 | if(this->header().needBeamSize()) |
---|
191 | beamCorrection = this->par.getBeamSize(); |
---|
192 | else beamCorrection = 1.; |
---|
193 | |
---|
194 | if(this->par.getSpectralMethod()=="sum"){ |
---|
195 | bool *done = new bool[xdim*ydim]; |
---|
196 | for(int i=0;i<xdim*ydim;i++) done[i]=false; |
---|
197 | // std::vector<Voxel> voxlist = this->objectList->at(objNum).pixels().getPixelSet(); |
---|
198 | std::vector<Voxel> voxlist = this->objectList->at(objNum).getPixelSet(); |
---|
199 | for(unsigned int pix=0;pix<voxlist.size();pix++){ |
---|
200 | int pos = voxlist[pix].getX() + xdim * voxlist[pix].getY(); |
---|
201 | if(!done[pos]){ |
---|
202 | done[pos] = true; |
---|
203 | for(int z=0;z<zdim;z++){ |
---|
204 | if(!(this->isBlank(pos+z*xdim*ydim))){ |
---|
205 | specy[z] += this->array[pos + z*xdim*ydim] / beamCorrection; |
---|
206 | if(this->reconExists) |
---|
207 | specRecon[z] += this->recon[pos + z*xdim*ydim] / beamCorrection; |
---|
208 | if(this->par.getFlagBaseline()) |
---|
209 | specBase[z] += this->baseline[pos + z*xdim*ydim] / beamCorrection; |
---|
210 | } |
---|
211 | } |
---|
212 | } |
---|
213 | } |
---|
214 | delete [] done; |
---|
215 | } |
---|
216 | else {// if(par.getSpectralMethod()=="peak"){ |
---|
217 | int pos = this->objectList->at(objNum).getXPeak() + |
---|
218 | xdim*this->objectList->at(objNum).getYPeak(); |
---|
219 | for(int z=0;z<zdim;z++){ |
---|
220 | specy[z] = this->array[pos + z*xdim*ydim]; |
---|
221 | if(this->reconExists) |
---|
222 | specRecon[z] = this->recon[pos + z*xdim*ydim]; |
---|
223 | if(this->par.getFlagBaseline()) |
---|
224 | specBase[z] = this->baseline[pos + z*xdim*ydim]; |
---|
225 | } |
---|
226 | } |
---|
227 | |
---|
228 | // long zdim = this->axisDim[2]; |
---|
229 | // Detection obj = this->objectList->at(objNum); |
---|
230 | // getSpecAbscissae(obj, this->head, zdim, specx); |
---|
231 | |
---|
232 | // float beamCorrection; |
---|
233 | // if(this->header().needBeamSize()) |
---|
234 | // beamCorrection = this->par.getBeamSize(); |
---|
235 | // else beamCorrection = 1.; |
---|
236 | |
---|
237 | // bool *mask = this->makeBlankMask(); |
---|
238 | // if(!this->reconExists) |
---|
239 | // for(int i=0;i<this->axisDim[2];i++) specRecon[i] = 0.; |
---|
240 | // if(!this->par.getFlagBaseline()) |
---|
241 | // for(int i=0;i<this->axisDim[2];i++) specBase[i] = 0.; |
---|
242 | |
---|
243 | // if(this->par.getSpectralMethod()=="sum"){ |
---|
244 | // getIntSpec(obj, this->array, this->axisDim, mask, beamCorrection, specy); |
---|
245 | // if(this->reconExists){ |
---|
246 | // getIntSpec(obj, this->recon, this->axisDim, mask, beamCorrection, specRecon); |
---|
247 | // } |
---|
248 | // if(this->par.getFlagBaseline()){ |
---|
249 | // getIntSpec(obj, this->baseline, this->axisDim, mask, beamCorrection, specBase); |
---|
250 | // } |
---|
251 | // } |
---|
252 | // else{ // if(.getSpectralMethod()=="peak"){ |
---|
253 | // getPeakSpec(obj, this->array, this->axisDim, mask, specy); |
---|
254 | // if(this->reconExists) |
---|
255 | // getPeakSpec(obj, this->recon, this->axisDim, mask, specRecon); |
---|
256 | // if(this->par.getFlagBaseline()) |
---|
257 | // getPeakSpec(obj, this->baseline, this->axisDim, mask, specBase); |
---|
258 | // } |
---|
259 | |
---|
260 | } |
---|
261 | //-------------------------------------------------------------------- |
---|
262 | |
---|
263 | } |
---|